chr16-84806348-C-A

Variant names:

• chr16-84806348-C-A
• rs8057431

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.776 in 151,960 control chromosomes in the GnomAD database, including 46,028 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.78 (46028 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.483

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.858 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.775 AC: 117738 AN: 151842 Hom.: 45964 Cov.: 30

Gnomad AFR AF: 0.865

Gnomad AMI AF: 0.725

Gnomad AMR AF: 0.840

Gnomad ASJ AF: 0.683

Gnomad EAS AF: 0.764

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.706

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.780

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.776 AC: 117860 AN: 151960 Hom.: 46028 Cov.: 30 AF XY: 0.775 AC XY: 57526 AN XY: 74254

Gnomad4 AFR AF: 0.866

Gnomad4 AMR AF: 0.840

Gnomad4 ASJ AF: 0.683

Gnomad4 EAS AF: 0.764

Gnomad4 SAS AF: 0.752

Gnomad4 FIN AF: 0.706

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.782

Alfa AF: 0.738 Hom.: 54059

Bravo AF: 0.790

Asia WGS AF: 0.771 AC: 2681 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.23
DANN	Benign	0.46

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs8057431; hg19: chr16-84839954;